<html>\r
-\r
+<head><title>Tree Calculation</title></head>\r
<body>\r
-<p><strong>UPGMA tree</strong></p>\r
-<p>If this option is selected then all sequences are used to generate a UPGMA \r
- tree. The pairwise distances used to cluster the sequences are the percentage \r
- mismatch between two sequences. For a reliable phylogenetic tree I recommend \r
- other programs (phylowin, phylip) should be used as they have the speed to use \r
- better distance methods and bootstrapping. Again, plans are afoot for a server \r
- to do this and to be able to read in tree files generated by other programs. \r
- <br>\r
- When the tree has been calculated a new window is displayed showing the tree \r
- with labels on the leaves showing the sequence ids. The user can select the \r
- ids with the mouse and the selected sequences will also be selected in the alignment \r
- window and the PCA window if that analysis has been calculated. </p>\r
-<p>Selecting the 'show distances' checkbox will put branch lengths on the branches. \r
- These branch lengths are the percentage mismatch between two nodes. </p>\r
-<p> </p>\r
-<p><strong>Neighbour Joining tree</strong></p>\r
-<p> The distances between sequences for this tree are generated in the same way \r
- as for the UPGMA tree. The method of clustering is the neighbour joining method \r
- which doesn't just pick the two closest leaves to cluster together but compensates \r
- for long edges by subtracting from the distances the average distance from each \r
- leaf to all the others. <br>\r
- Selection and output options are the same as for the UPGMA tree.<br>\r
+<p><strong>Calculation of trees from alignments</strong></p>\r
+<p>Trees are calculated on either the complete alignment, or just the\r
+currently selected group of sequences, using the functions in the\r
+<strong>Calculate→Calculate tree</strong> submenu. There are\r
+four different calculations, using one of two distance measures and\r
+constructing the tree from one of two algorithms :\r
+</p>\r
+<p><strong>Distance Measures</strong></p>\r
+<p>Trees are calculated on the basis of a measure of similarity\r
+between each pair of sequences in the alignment :\r
+<ul>\r
+<li><strong>PID</strong><br>The percentage identity between the two\r
+sequences at each aligned position.\r
+<li><strong>BLOSUM62</strong><br>The sum of BLOSUM62 scores for the\r
+residue pair at each aligned position.\r
+</ul>\r
+</p>\r
+<p><strong>Tree Construction Methods</strong></p>\r
+<p>Jalview currently supports two kinds of agglomerative clustering\r
+methods. These are not intended to substitute for rigorous\r
+phylogenetic tree construction, and may fail on very large alignments.\r
+<ul>\r
+<li><strong>UPGMA tree</strong><br>\r
+ UPGMA stands for Unweighted Pair-Group Method using Arithmetic\r
+ averages. Clusters are iteratively formed and extended by finding a\r
+ non-member sequence with the lowest average dissimilarity over the\r
+ cluster members.\r
+<p></p>\r
+</li>\r
+<li><strong>Neighbour Joining tree</strong><br>\r
+ First described in 1987 by Saitou and Nei, this method applies a\r
+ greedy algorithm to find the tree with the shortest branch\r
+ lengths.<br>\r
+ This method, as implemented in Jalview, is considerably more\r
+ expensive than UPGMA.\r
+</li>\r
+</ul>\r
</p>\r
+<p>A newly calculated tree will be displayed in a new <a\r
+href="../calculations/treeviewer.html">tree viewing window</a>. In\r
+addition, a new entry with the same tree viewer window name will be added in the Sort\r
+menu so that the alignment can be reordered to reflect the ordering of\r
+the leafs of the tree. If the tree was calculated on a selected region\r
+of the alignment, then the title of the tree view will reflect this.</p>\r
+\r
+<p><strong>External Sources for Phylogenetic Trees</strong></p>\r
+ <p>A number of programs exist for the reliable construction of\r
+ phylogenetic trees, which can cope with large numbers of sequences,\r
+ use better distance methods and can perform bootstrapping. Jalview\r
+ can read <a\r
+ href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>\r
+ format tree files using the 'Load Associated Tree' entry of the\r
+ alignment's File menu. Sequences in the alignment will be\r
+ automatically associated to nodes in the\r
+ </p>\r
+\r
+\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff